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Thread: Abstracts from SMBE 2017

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    Abstracts from SMBE 2017

    Abstracts from SMBE 2017 are available now: http://www.smbe2017.org/wp-content/u...ok-22-June.pdf

    I will post relevant abstracts here, feel free to add the ones that you find interesting.

    Ancient DNA from Two Pre-Columbian Mummies from Sierra Tarahumara

    Viridiana Villa-Islas1,*, Cristina Valdiosera2, Rosa Fregel3, Alexandra Sockell3, Mattias Jakobsson4, Andres Moreno-Estrada5, Carlos Bustamante3, María C Ávila-Arcos1

    1 Population and Evolutionary Genomics Lab, International Laboratory for Human Genome Research, UNAM, Mexico, Queretaro, Mexico,
    2 Department of Archaeology and History, La Trobe University, Melbourne, Australia,
    3 Department of Genetics, Stanford University, California, United States,
    4 Department of Evolutionary Biology, Uppsala University,
    Uppsala, Sweden,
    5 Human Evolutionary and Population Genomics Lab, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO),, Irapuato, Mexico

    Abstract: The Tarahumara are an indigenous population also known as Rarámuri, who inhabits the Sierra Tarahumara, mainly in the state of Chihuahua, Mexico. This millenary group is recognized for their incredible physical endurance and ability to run long distances. Genomic studies of this population and its ancestors may give us insights into their population history. Here we report the retrieval and sequencing of aDNA from two ca. 900 year-old pre-Columbian mummies found in a cave from Sierra Tarahumara. We performed Whole-Genome-Capture on the aDNA libraries to enrich the amount of endogenous DNA and sequenced until we reached saturation. We obtained enough data to cover two-thirds of the genome for one of the mummies and less than 10% for the second. This allowed us to perform PCA to compare the ancient individuals with modern Native Mexican groups. Preliminary analyses show that the mummies cluster with different present-day populations, respectively. This opens up questions of historical and anthropological interest; specifically regarding past genetic structure and migration between different indigenous groups.

    Expanded summary*: The Tarahumara are an indigenous population also known as Rarámuri, who inhabits the Sierra Tarahumara, mainly in the state of Chihuahua, Mexico. Long-distance running is a cultural practice that men, women and children have practiced for centuries through the rugged landscape of the Sierra Tarahumara. Motivated by the interest in investigating a possible genetic basis for this extraordinary capacity, and to learn more about their population history, we launched a genomic study of this population combining genomic information from past and present individuals.

    Ancient DNA (aDNA) offers an unparalleled source of information to better understand the evolutionary processes that have generated the genetic diversity of today’s populations and to detect possible genes that could have been subject to selection in “real time”. To gain insights into the population history of the Rarámuri and to explore possible signatures of adaptive evolution, we increased the sequencing depth of two ancient genomes belonging to two ca. 900-year old pre-Columbian mummies initially reported in Raghavan et al, 2015. Both mummies were found in a cave from Sierra Tarahumara; their DNA was extracted, built into Illumina libraries and sequenced at low depth. We increased the coverage of their genomes by generating additional libraries and performing Whole-Genome Capture (WGC) to enrich their endogenous content.

    We obtained enough data to cover two-thirds of the genome for one of the mummies and less than 10% for the second. This allowed us to determine the mitochondrial haplogroup of the two individuals as C, and C1c1a, respectively; both are typical mitochondrial haplogroups of Native Americans. Also, we performed PCA to compare the ancient individuals with a reference panel of modern Native Mexican groups. Interestingly, these preliminary analyses show that one mummy clusters closely with present-day Tarahumaras, while the second clusters with a geographically distant population. This result opens up questions of historical and anthropological interest; specifically regarding past genetic structure and migration between different indigenous groups and demands further and more detailed analyses of the genomic data in a population context.

    In the next phase of the project we will increase the depth of coverage of the genomes and combine with knowledge generated from modern Rarámuri. We are in parallel characterizing functional variation in present-day Rarámuri and identifying targets of adaptive evolution. The combination of both sources of genetic information — ancient and modern — might help characterize the temporality of the variants associated with adaptive evolution, which might, or might not, be related to physical endurance.

    This study, not only complements our knowledge on the genetic component of the Tarahumara population, but also contributes to a better understanding of the pre-Columbian Mexican native populations, which have been little studied from the point of view of genetic diversity. Few studies to date have focused on the paleogenomic study of ancient human samples in the Americas and none has characterized complete ancient genomes of samples from Mexico despite its rich historical and cultural heritage as reflected in the vast archaeological record. Consequently, paleogenomic studies in Mexico have a great potential.

    Furthermore, another important contribution of this study is the implementation of the WGC enrichment method, which has been proposed to increase the endogenous DNA content of ancient human samples, yet it has not been tested thoroughly. This work allows testing new parameters of the protocol and gain further insights about its performance on mummified samples.



    Complete mitochondrial genomes provide additional evidence on the geographical origin of the indigenous people of the Canary Islands

    Rosa Fregel1,*, Alejandra C. Ordóńez2, André E. R. Soares3, Jonathan Santana4, Matilde Arnay2, Beth Shapiro3, Carlos D. Bustamante1

    1 Department of Genetics, Stanford University, Stanford, United States,
    2 Department of Prehistory, Universidad de La Laguna, La Laguna, Spain,
    3 Paleogenomics Lab, University of California Santa Cruz, Santa Cruz, United States,
    4 Department of Prehistory, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain

    Abstract: Deciphering the geographic origin of the Canary Islands’ indigenous inhabitants has fascinated both scholars and the general public. Ancient DNA (aDNA) evidence, based on PCR techniques, has confirmed the presence of North African mitochondrial DNA (mtDNA) lineages in the indigenous people, including the North African U6 haplogroup. In fact, one striking result was the discovery of the U6b1a sub-haplogroup, which is exclusively observed in ancient and modern populations of the Canary Islands, and it is absent in North Africa. Classical aDNA techniques have provided valuable information, but results have been always hindered by the risk of modern contamination. Moreover, PCR-based analyses are limited to a small portion of the mtDNA genome and important information from the coding region is unavailable.

    In this study, we apply for the first time next-generation sequencing to the recovery of whole mtDNA genomes of indigenous people of the Canary Islands (n=44). Most of the lineages observed in the ancient population of the Canary Islands belong to West Eurasian and North African haplogroups, confirming previous results. As expected from archaeological, anthropological and linguistic studies, the majority of indigenous mtDNA lineages are present in the Maghreb. Phylogenetic analysis indicates the presence of additional autochthonous lineages that mimic the distribution observed for U6b1a. Coalescence ages for those Canarian-autochthonous subhaplogroups are mostly in agreement with the colonization time proposed by radiocarbon dates and archaeological criteria. However, an older autochthonous lineage as U6b1a is unlikely to have developed in the Canary Islands based on currently available archaeological records.

    Expanded summary*: The goal of this project is to apply paleogenomic techniques to the study of the Canary Islands’ prehistory for the first time. During the 13th-14th centuries, European sailors eagerly traveled the oceans searching for new worlds. The subsequent expansion of European colonies across the world, triggered the European dominance of the global economy, but also had important cultural and ecological consequences, because it brought together, for the first time, distant civilizations and environments. Portuguese sailors discovered several groups of islands in the Atlantic Ocean in the 13th century. Around this time, the Portuguese and Castilians began to settle the Atlantic archipelagos, including the Azores, Madeira and Cape Verde, but only the Canary Islands were found to be inhabited by an indigenous population, generally known as Guanches. During the 15th century, the Canary Islands were gradually conquered, directly or indirectly, by the Spanish kingdom of Castile, beginning with the island of Lanzarote in 1402 and finishing with Tenerife in 1496. In general terms, the Conquest was exceptionally violent, due in part to the fierce resistance of the indigenous people against the invaders. The crushing of the resistance, and the subsequent European colonization, had a great impact on the indigenous way of life. In spite of the indigenous protective policy of Queen Isabel ‘La Católica’, who legally abolished slavery on the Islands in 1498, a large number of Guanches were deported during and after the Conquest, and some of them were introduced into the 16th century European slave trade. Those that survived and stayed within the islands progressively mixed with the European colonizers, leading to the loss of indigenous culture and language.

    Most archaeological, anthropological and linguistic researchers point to a North African origin for the Canary indigenous people, more precisely related to the proto-Berber and Berber world. Ancient DNA analyses on the Guanche population using classical PCR-based methods have confirmed the presence of North African lineages in the indigenous people, including different sublineages of the characteristic North African U6 haplogroup. One important result was the characterization of the U6b1a sub-haplogroup, which is exclusively observed in ancient and modern populations of the Canary Islands, and not in North Africa. However, due to the lack of samples from the eastern islands (Gran Canaria, Lanzarote and Fuerteventura) and to limitations associated with the use of only a small portion of the mtDNA genome, we were unable to identify a specific geographical origin for the Guanche people.

    In this project, we used next-generation sequencing to generate complete mtDNA genomes from the indigenous population for the first time. We obtained high-coverage mtDNA genomes for 44 human remains excavated from 23 different archaeological sites distributed across the entire Canarian archipelago. Most of the lineages observed in the ancient population of the Canary Islands belong to West Eurasian (H, J and T) and North African (U6) haplogroups, confirming previous results using PCR techniques. As expected from archaeological, anthropological and linguistic studies, our results indicate that the first inhabitants of the Canary Islands are related to modern populations of North Africa. However, the absence or low frequency of some key haplogroups in North Africa indicates that the continental genetic composition has been modified by later human migrations. More strikingly, phylogenetic analysis indicates the presence of additional autochthonous lineages that mimic the distribution observed for U6b1a. By using whole-genome sequences of indigenous samples, we have been able to identify additional autochthonous lineages that mimic the distribution observed for U6b1a. Those Canarian-specific haplogroups are sublineages of the Eurasian H, J and T, and the African L3 macrohaplogroups. With this refined phylogeographic information we will be able to unequivocally assess the indigenous origin of maternal lineages observed in the modern Canarian population.

    Apart from its clear significance for understanding the demographic history of the Guanche population, the results obtained in this project are also of paramount importance for the Canarian society. The success of projects and companies providing ancestry information indicates how people crave knowledge about their origin. This is especially true for the Canary Islands. The indigenous population plays an important role on the identity of the modern inhabitants of the Canary Islands, who are very interested in knowing as much as possible about this part of their history. However, due to the mystical aura that has always surrounded the Guanche population since the first European chroniclers started writing about them, misleading and pseudo-scientific information is sometimes fed to the public and accepted as fact. It is the responsibility of scientists to provide society with evidence and help providing insight to differentiate what is fact and what is myth. This project will allow us to keep answering those questions with state-of-the-art methods in the field.

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    7,000 years of change: Migration and admixture in the population history of the Caribbean

    Maria A Nieves-Colon1,*, William J Pestle2, Jada Benn-Torres3, Carlos D Bustamante4, Anne C Stone1

    1 School of Human Evolution and Social Change, Arizona State University, Tempe, AZ,
    2 Department of Anthropology, University of Miami, Coral Gables, FL,
    3 Vanderbilt University, Nashville, TN,
    4 Department of Genetics, Stanford University, Stanford, CA, United States

    Abstract: Although the Caribbean has been continuously inhabited for the last 7,000 years, European contact in the last 500 years dramatically reshaped the cultural and genetic makeup of island populations. Several recent studies have explored the genetic diversity of Caribbean Latinos, and have characterized Native American variation present within their genomes. However, the difficulty of obtaining ancient DNA from pre-contact populations and the underrepresentation of non-Latino Caribbean islanders in genetic research, have prevented a complete understanding of genetic variation over time and space in the Caribbean basin. Here we discuss research that takes two approaches towards characterizing migration and admixture in Caribbean populations: an ancient DNA analysis of 139 individuals from three pre-contact archaeological sites in Puerto Rico (A.D. 500–1300), and an analysis of whole genome variants from 55 Afro-Caribbeans in five Lesser Antillean populations. Our ancient DNA analysis traces the origin and number of pre-contact migrations to Puerto Rico and examines the extent of genetic continuity between ancient and modern populations. In contrast, our modern DNA work analyzes autosomal SNP genotypes to characterize complex patterns of admixture since European contact among Lesser Antillean Afro-Caribbeans. Our findings characterize how ancient indigenous groups, European colonial regimes, the African Slave Trade and modern labor movements have shaped the genomic diversity of Caribbean islanders. In addition to its anthropological or historical importance, such knowledge is also essential for informing the identification of medically relevant genetic variation in these populations.

    Expanded summary*: Characterizing how migration and admixture shapes human genetic diversity is vital for understanding human evolution, history and health. This is especially true in world regions that have undergone recent and dramatic demographic shifts, such as the Caribbean. Previous research with admixed Caribbean populations has shown that many islanders retain genomic variation from pre-Columbian indigenous groups, but also carry signatures of more recent admixture events fostered by European colonization and the African Slave Trade. However, a complete understanding of human genomic diversity across the Caribbean region is hampered by sampling gaps of both past and present populations. Due to the difficulties of obtaining ancient DNA (aDNA) from the tropics, the genetic diversity of pre-Columbian Caribbean groups is not well characterized. Efforts have been made to address this problem by studying Native American fragments in the genomes of admixed islanders. But, because modern populations do not retain all the genomic diversity of ancient groups, this approach provides limited resolution for reconstructing ancient demographic events. Further, many Caribbean populations remain underrepresented in large catalogs of genomic variation. Except for Barbadian Afro-Caribbeans, recently included in 1000 Genomes Phase 3, genetics research on Lesser Antillean populations has been limited to uni-parental loci and low-density ancestry informative markers. The present research seeks to fill in these gaps through two approaches: an aDNA analysis of 139 individuals from three archaeological sites in Puerto Rico (A.D. 500–1300), and an analysis of genome-wide SNP variants from 55 Afro-Caribbeans in five Lesser Antillean (LA) populations.

    The aDNA investigation characterizes patterns of migration and genetic admixture in pre-Columbian Puerto Rico, and examines the extent of genetic continuity between ancient groups and modern islanders. In-solution capture and next-generation sequencing were used to obtain ancient DNA from 139 human skeletal remains (dated between A.D. 500–1300), from the sites of Tibes (n=52), Paso del Indio (n=50) and Punta Candelero (n=37). Preliminary data obtained from 24 complete mitochondrial genomes (mean read depth: 9.8x) suggest that pre-Columbian communities in Puerto Rico share genetic affinity with several extant South American and Mesoamerican indigenous populations. We also find that most pre-Columbian mtDNA lineages are not present in the Americas today, except for one, which is found almost exclusively in modern Puerto Ricans. These data support an origins scenario of complex and continuous admixture for ancient Caribbean groups but also underscore the large effect that contact-era population declines had on indigenous communities. Autosomal genotypes currently being generated from these remains will further inform these issues.

    The second part of our project analyzes autosomal SNP genotypes in 55 self-identified Afro-Caribbeans from St. Kitts (n=5), St. Lucia (n=10), St. Vincent (n=15), Grenada (n=6), and Trinidad (n=19). We characterize patterns of genome-wide variation and ancestry in these individuals and compare them to exising data from other recently admixed American populations. We observe a complex pattern of admixture among in the LA Afro-Caribbeans with inputs from up to five continental sources and strong signatures of sex-biased mating. African ancestry proportions are high, but Native American ancestry is extremely low. This pattern contrasts sharply with that observed in Caribbean Latinos and is more similar to that observed in Haitians and Barbadians. We further observe that Trinidadian Afro-Caribbeans have the highest proportion of admixture with East and South Asian populations of all Caribbean populations studied to date.

    Overall, our findings underscore the large impact of post-contact demographic shifts on Caribbean population history and illustrate how genomic diversity has changed in this region over the last 7,000 years. In addition, this work increases the representation of admixed and diverse populations in available genomic datasets and has the potential to inform future functional and clinical genetics research with admixed Caribbean islanders.



    Genome wide data from the Iron Age provides insights into the population history of Finland.

    Thiseas Christos Lamnidis1,*, Kerttu Majander2, Elina Salmela1 3, Anna Wessman4, Antti Sajantila5, Päivi Onkamo3, Stephan Schiffels1, Johannes Krause1 2

    1Department of Archaogenetics, Max Planck Institute for the Science of Human History, Jena,
    2Institute for Archaeological Sciences, Archaeo-and Palaeogenetics, University of Tübingen, Tübingen, Germany,
    3 Department of Biosciences,
    4 Department of Archaeology,
    5 Department of Forensic Medicine, University of Helsinki, Helsinki, Finland

    Abstract: The population history of Finland is subject of an ongoing debate, in particular with respect to the relationship and origins of modern Finnish and Saami people. Here we analyse genome-wide data, extracted from three teeth found in the archaeological site of Levänluhta, in southern Ostrobothnia. The site dates back to the Iron Age between 550-800 AD, according to the artefacts recovered, while radiocarbon dating on scattered femurs from the site span 350-730 AD. When analysed together with previously published ancient European samples and with modern European populations, the ancient Finnish samples lack a genetic component found in early Neolithic Farmers and all modern European populations today. Instead, we find that they are more closely related to modern Siberian and East Asian populations than modern Finnish are, a pattern also observed in genetic data from modern Saami. Our results suggest that the ancestral Saami population 1500 years ago, inhabited a larger region than today, extending as far south as Levänluhta. Such a scenario is also supported by linguistic evidence suggesting most of Finland to have been speaking Saami languages before 1000 AD. We also observe genetic differences between modern Saami and our ancient samples, which are likely to have arisen due to admixture with Finnish people during the last 1500 years.



    The genetic history of the Indonesian Pygmies of Flores

    Serena Tucci1 2,*, Benjamin Vernot3, Rajiv C. McCoy1, Samuel Vohr4, Matthew R. Robinson5, Chiara Barbieri6, Joshua Schraiber7 8, Herawati Sudoyo9 10, Peter M. Visscher5 11, Guido Barbujani2, Richard E. Green4, Joshua M. Akey1

    1 Department of Genome Sciences, University of Washington, Seattle, United States,
    2 Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy,
    3 Department of Evolutionary Genetics, Max Planck Institute for
    Evolutionary Anthropology, Leipzig, Germany,
    4 Department of Biomolecular Engineering, University of California, Santa
    Cruz, United States,
    5 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia,
    6 Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany,
    7 Institute for Genomics and Evolutionary Medicine,
    8 Department of Biology, Temple University, Temple, United States,
    9 Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology,
    10 Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia,
    11 Queensland Brain Institute, The University of Queensland, Brisbane, Australia

    Abstract: Modern human pygmy populations are distributed globally, and their short stature is hypothesized to represent one aspect of a complex eco-geographic adaptation to rainforest or island environments. Although numerous genetic studies have been conducted on pygmies in Africa and Southeast Asia, to date, there have been no genome-scale analyses of the pygmy population living on the island of Flores, Indonesia. Intriguingly, this population lives in a village near the cave where remains of a small-bodied human species, Homo floresiensis, were recently found. Here, we describe whole-genome sequences (>40x) from 10 Flores pygmy individuals, as well as genome-wide SNP data from 35 individuals. The Flores genomes harbor on average 48 Mb and 4.4 Mb of Neandertal and Denisovan sequence, respectively. Height-associated loci identified in European populations are significantly differentiated in the Flores pygmies, who possess an excess of height-decreasing alleles and a deficiency of height-increasing alleles. This result is consistent with a hypothesis of polygenic selection acting on standing variation for reduced stature in Flores. Finally, we identify a strong signature of recent positive selection encompassing the FADS gene cluster on chromosome 11, encoding for fatty acid desaturases that regulate the metabolism of long-chain polyunsaturated fatty acids (LC-PUFA). Flores individuals are nearly fixed for an ancestral haplotype that is predicted to confer reduced capacity to synthesize LC-PUFA from plant-based precursors. Our results add to emerging evidence that the FADS region has been a recurrent target of selection in diverse human populations, possibly in response to changing diets.

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    Ancient Iberian and Central European Yersinia pestis genomes reveal genetic diversity of the Justinianic Plague

    Marcel Keller1 2,*, Maria A. Spyrou1 3, Brigitte Haas-Gebhard4, Bernd Päffgen5, Jochen Haberstroh6, Albert Ribera7, Kathrin Nägele1, Bernd Trautmann2, Joris Peters2 8, Alexander Herbig1, Kirsten Bos1, Michael McCormick9, Michaela Harbeck2, Johannes Krause1

    1 Department Archaeogenetics, Max Planck Institute for the Science of Human History, Jena,
    2 State Collection of Anthropology and Palaeoanatomy, Bavarian Natural History Collections, Munich,
    3 Institute for Archaeological Sciences, Archaeo-and Palaeogenetics, University of Tübingen, Tübingen,
    4 Archaeological Collection of the Bavarian State,
    5 Institute for Pre-and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilian University Munich,
    6 Bavarian State Department of Monuments and Sites, Munich, Germany,
    7 Department for Municipal Archaeology, Valencia City Council, Valencia, Spain,
    8 Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University Munich, Munich, Germany,
    9 Initiative for the Science of the Human Past, Department of History, Harvard University, Cambridge, United States

    Abstract: The Justinianic Plague (541-750 CE) was a pandemic that contributed to the end of Antiquity, probably entering the Roman Empire at the Red Sea and spreading through and beyond it. Recently molecular evidence from two Early Medieval grave fields (Aschheim & Altenerding) in SE Germany identified Yersinia pestis as the likely causative agent of the Justinianic Plague. Phylogenomic analysis showed the Central European 6 th century Justinianic strains to form a previously unknown branch in the bacterial phylogeny, distinct from the lineage associated to the second pandemic that followed the Black Death (1348 -1351 CE). Here, we present the first genomic data of Y. pestis from the western part of the Mediterranean (Valencia, Spain) as well as new Y. pestis genomes from multiple sites in Central Europe from the 6th to 7th century. We confirm a common origin for all Justinianic strains sequenced to date, but demonstrate novel aspects of its evolution. Additionally, the phylogenetic analysis suggests at least two independent waves of plague in Central Europe, both unknown in contemporary records. In contrast to what is known regarding the second pandemic following the Black Death, we observe the formation of multiple plague lineages that reflect different epidemiological patterns.


    40,000-year-old individual from Asia provides insight into early population structure in Eurasia

    Melinda Yang1 2,*, Xing Gao1, Ayinuer Aximu Petri1 3, Haowen Tong2, Birgit Nickel3, Matthias Meyer1 3, Svante Pӓӓbo1 3, Janet Kelso1 3, Qiaomei Fu1 2

    1 Laboratory on Molecular Paleontology, Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology,
    2 Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China,
    3 Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    Abstract: To date, very few ancient genomic studies have been conducted in Asia. Genome-wide studies using ancient individuals from Europe have revealed complex ancestry and genetic structure in ancient populations that could not be observed studying only present-day populations, suggesting similar approaches may also aid in elucidating the demographic history in Asia. Here, we present genome-wide data for a 40,000-year-old individual from Tianyuan Cave near Beijing, China. We show that he is more related to present-day Asians than present-day and ancient Europeans. However, unlike present-day Asians, he shows potential relationships with some present-day South Americans and a 35,000-year-old European individual. Our results suggest that there was extensive population structure in Asia by 40,000 years ago that persisted over an extended period of time.



    Reconstructing prehistoric African population structure and adaptation

    Pontus Skoglund*, Alissa Mittnik, Kendra Sirak, Mateja Hajdinjak, Nadin Rohland, Swapan Mallick, Tasneem Salie, Anja Heinze, Matthias Meyer, Alexander Peltzer, Matthew Ferry, Eadaoin Harney, Megan Michel, Kristin Stewardson, Jessica Cerezo-Roman, Crissy Chiumia, Alison Crowther, Elizabeth Gomani-Chindebvu, Richard Helm, Mark Horton, Alan Morris, John Parkington, Mary E Prendergast, Raj Ramesar, Ceri Shipton, Jessica Thompson, Ruth Tibesasa, Vanessa Hayes, Svante Pääbo, Nick Patterson, Nicole Boivin, Ron Pinhasi1, Johannes Krause, David Reich

    1Department of Anthropology, University of Vienna, Vienna, Austria

    Abstract: The population genomic landscape of Africa prior to its transformation by expansions of farmers and pastoralists is poorly understood, partly due to poor ancient DNA preservation and partly due to the deep time scale of human population history on the continent. We assembled genome-wide data from ten sub-Saharan Africans who lived in the last 4,500 years, and show that one of the most deeply divergent present-day human lineages that is today found almost exclusively in people living in southern Africa, was in the past 2,000 years also present in populations much farther north in Malawi and the Zanzibar archipelago. These results highlight the existence of an ancient genetic cline stretched over thousands of kilometers along a south-north axis. By leveraging data from ancient African genomes without ancestry from more recent into-Africa migrations, we show that western Africans today may harbor ancestry from a lineage that separated from other modern human lineages earlier than any other, including the Khoe-San of southern Africa. Finally, we use the availability of time-stratified southern African genomes to document evidence of both selective sweeps and polygenic selection that might have conferred adaptations to desert environments.

    Expanded summary*: Africa is the homeland of our species, and contains within it more human genetic diversity than the rest of the world combined. However, far less is known about the prehistory of Africa than the prehistory of other parts of the world, both because of the poor preservation of ancient DNA in Africa’s hot climate, and because of the disruptions of African population structure that occurred with the expansion of farming populations. Here we increase the amount of ancient DNA from Africa by a factor of 10 by taking advantage of recent advances for extracting DNA from ancient individuals. Using this first view of prehistoric African population structure, we provide evidence for a previously unknown hunter-gatherer population that once dominated East Africa, and the existence of an admixture gradient in which ancient East African foragers where in contact with southern African foragers as far north as Tanzania. In contrst, today such ancestry is restricted to the southern tip of Africa.. We also show evidence that West Africans today harbor substantial ancestry from a lineage that split from other modern humans before the lineage currently viewed as oldest (the Khoe-San of southern Africa). Finally, we reveal recent natural selection in the Khoe-San of southern Africa today that may have provided key adaptations to life in the open Kalahari desert, including genes affecting response to radiation and taste receptor loci. These results will provides the first view of prehistoric African population structure, and represent a first ancient genomic step into the deep past of humans in Africa.

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    Ancient genomics of pre-Columbian North American dogs

    Laurent Frantz1,*, James Haile1, Greger Larson1

    1 University Of Oxford, Oxford, United Kingdom

    Abstract: Dogs were the first species to be domesticated ~15,000 ago, several thousand years before the advent of settled agriculture. In the New World, the first unequivocal dog remains date to >9,000BP, and previous studies suggested that early American dogs were transported by people arriving from the Old World and were not independently derived from New World wolves. European domestics then largely replaced the early North American dogs, though modern New World dogs may retain a degree of ancestry from the first American dogs. This suggestion remains controversial, however, since the nuclear ancestry of pre-Columbian American dogs has yet to be established. As a result, it remains possible that dogs were domesticated independently in the New World before being replaced by dogs from either Asia or Europe. To test this, we generated four high coverage (and multiple low coverage) genomes from ancient North American dogs including some of the earliest dog remains on the continent (>9,000BP). These data allowed us to assess whether dogs were independently domesticated in North America, when they were replaced by Eurasian dogs, how many times they were replaced, and the degree of extant pre-Columbian ancestry in modern North American dogs. Lastly, this data allow us to characterise the demographic and adaptive history of this isolated population of domestic dogs.



    Ancient mitogenomes of Argentine Patagonia (6070-310 YBP) reveal the early contribution of lineages not previously found in South America

    Maria Laura Parolin1,*, Rosa Irene Fregel Lorenzo2, Claudio Marcelo Bravi3, Fernando Luis Mendez2, Silvia Lucrecia Dahinten1, Julieta Gómez Otero1, Beth Shapiro4, Richard Edward Green4, Camila Tamburrini1, Néstor Guillermo Basso1, Carlos Bustamante2

    1 Instituto de Diversidad y Evolución Austral, CENPAT-CONICET, Puerto Madryn, Argentina,
    2 Department of Genetics, Stanford University, Stanford, United States,
    3 Instituto Multidisciplinario de Biología Molecular , CONICET CICPBA: UNLP, La Plata, Argentina,
    4 Paleogenomics Lab, University of California Santa Cruz, Santa Cruz, United States

    Abstractatagonia, a cul-de-sac for the continental dispersal of Homo sapiens into the Americas, has been extensively analyzed by archaeologists and bioanthropologists. Despite its deep and rich archaeological record, the genetic make-up of its pre-contact inhabitants is barely known. We present the analysis of 19 mitogenomes recovered by NGS from archaeological sites in Central Patagonia (Chubut, Argentina). 15 are pre-contact samples, (6,010-770YBP), and four are samples from historical times (550-310YBP). Preservation of the samples was extraordinary, with endogenous DNA values up to 68%. Preliminary analysis indicates that mtDNA genomes from Central Patagonia belong to haplogroups B2 (21%), C1b (21%), C1c (5%), D1 (47%) and D4h3a (5%). This is surprising when compared with a database of >19,000 control region sequences and >2,100 mitogenomes of Native American origin: 1) While modern indigenous populations from Northern and Central Patagonia of Argentina and Chile derive 41-54% of their maternal lineages from clades B2i2 and C1b13, none of these are present in our dataset; 2)75% of our B2 and C1b lineages share derived polymorphism with lineages so far known to be present only in modern Central-Western Argentina; and 3) although modern Patagonians carry the highest continental frequencies of D1g, the ancient set is enriched mostly in D1g5, a lineage widely distributed from South-Central Andes to Tierra del Fuego (including two samples with private motifs not described before). The upcoming analysis of the nuclear portion of these samples will help us better understand migratory and admixture processes in the Patagonian region.

    Expanded summary*: As mentioned in the abstract, this research constitutes the first analysis of complete ancient mtDNA genomes of Argentine Patagonia (6070-310 YBP) revealing the early contribution of lineages not previously found in South America, and it will represent a great opportunity to discuss it with peers in the SMBE meeting.

    The Austral Evolution and Diversity Institute (Instituto de Diversidad y Evolución Austral-IDEAus) in Centro Nacional Patagonico (CENPAT-CONICET), where I have been a researcher since 2012, is located in Patagonia Argentina. During the last 10 years, I have been leading and collaborating in different bio-anthropological research projects whose main goal is to increase our understanding of the “genetic identity” of the Argentinean population, trying to demystify the widespread belief that the country may have the highest European ancestry in South America. On the contrary, several anthropo-genetic studies from different regions of the country demonstrated that the native component increases towards the north and south of the country while the European component is concentrated in the center of Argentina.

    During the last 7 years, I have been devoted almost exclusively to the anthropo-genetic and demographic study of urban and rural not previously studied populations from Patagonia. My interest arises not only from the fact that I am native of Patagonia, but also because this region is one of the least studied places in terms of its genetic characterization. Focusing on singularities as a result of different migratory histories and differential admixture processes in each locality. In collaboration with archeologists, anthropologists, and geneticists from the IDEAus, we recently started a new research project to use genetics in study of past Patagonian populations. Anthropologists from IDEAus have worked for more than 25 years in the recovery and study of human remains and artifacts associated with the lifestyle of hunter-gatherer populations from Patagonia (called Tehuelche), which inhabited the centro-coastal region. As mentioned in the abstract, both, the history of human settlements in South America and the biological diversity of the hunter-gatherer populations inhabiting the southern tip of the continent, have been extensively studied by researcher from multiple disciplines. Recently, two archaeological sites that evidence early human settlements in Chile and Argentina (14,500 BP) have been reported. However, there is to date scarce genetic information available from the early human populations of Argentina, and in particular, from the Patagonia region.

    Thanks to a fellowship granted by CONICET, to the support of Dr. Carlos Bustamante and his team (Department of Genetics, Stanford University), and to that of the Paleogenomics Lab at the University of California Santa Cruz (for the processing of the archaeological samples), I have been able to retrieve information on new mitochondrial lineages. While we have sequenced 19 individuals in this work. IDEAus holds an osteological collection with more than 120 samples from individual and common burials, all of which are archaeologically contextualized with dates ranging from the Middle to the Late Holocene and from historical times. The upcoming analysis of this large collection (the largest in Patagonia) will contribute to a broader understanding of evolutionary and population processes involving Homo sapiens populations as they migrated to the southern end of the Americas. Given the novelty of our results and its relevance to some of the major topics in the 2017 SMBE meeting, attending this event would constitute a great personal opportunity to present the result of our aDNA work in an international meeting. Likewise, the annual SMBE meeting is particularly important for young researchers, especially for Latin America, because it allows us to present our work to an expert audience and provides us with the opportunity to enlarge our networks and create fruitful connections, like the one that made this project possible.




    The Role of Migration in Cultural Changes during the Chalcolithic period in the Levant

    Eadaoin Harney1,*, Hila May2, Israel Hershkovitz2, Dina Shalem3, Nadin Rohland4, Swapan Mallick4, Iosif Lazaridis4, Nick Patterson4 5, David Reich4 5 6

    1 Organismic and Evolutionary Biology, Harvard University, Cambridge, United States,
    2 Anatomy and Anthropology, Tel Aviv University, Tel Aviv,
    3 The Institute for Galilean Archaeology, Kinneret, Israel,
    4 Genetics, Harvard Medical School, Boston,
    5 Broad Institute, Cambridge,
    6 Howard Hughes Medical Institute, Boston, United States

    Abstract: A major controversy is whether cultural change evident in the archaeological record is typically achieved through movements of people or cultural infiltration. The Chalcolithic period in the southern Levant (4th-5th millennium BCE) contains artifacts not detected in earlier archaeological sites of the region, yet have strong affinities to contemporary and earlier cultures from Anatolia and Iran. In order to test the hypothesis that the Chalcolithic culture of this region may have been formed through migration from the North, we analyzed new genome-wide ancient DNA data from 22 individuals from the Peqi'in cave site in Upper Galilee, Israel that are associated with the Late Chalcolithic culture of the southern Levant, thereby approximately doubling the number of samples with genome-wide ancient human DNA from the Levant. We report that that these individuals derive approximately 58% of their ancestry from populations related to those of the local Levant Neolithic, approximately 17% from populations related to the Iran Chalcolithic, and approximately 25% related to the Anatolian Neolithic, supporting the hypothesis that this population was formed in part by migration from the North. We show that population turnover continued after the Chalcolithic, as the population that the Peqi'in Cave group was a part of did not contribute to later Levantine populations from the Bronze Age, which had little or no Anatolian-related ancestry.

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    A genetic compendium of an island: documenting continuity and change across Irish prehistory

    Lara Cassidy1,*

    1Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland

    Abstract: Throughout the 10,000 year human occupation of Ireland, the island has witnessed several profound cultural shifts. The first four ancient Irish genomes published demonstrate that two pivotal transitions, that to agriculture and later to metallurgy, were both catalyzed by extensive population migration to the island. Moreover, both Y-chromosome and haplotype-based analyses suggest continuity between Irish Bronze Age genomes and modern Celtic-speaking populations. Adding to these conclusions, data is presented here from over 50 ancient Irish genomes (>1X) spanning from the Mesolithic to Late Iron Age (4500 BC –500 AD). Through a combination of pseudo-diploid analyses (PCA, ADMIXTURE, D-and F-statistics) and haplotype-sharing methods, applicable through the use of genotype imputation, this dataset both confirms our published results and offers a more detailed view of the genetic processes surrounding these transitions. We explore the impact of hunter-gatherer introgression on early farming populations; the possibility of geographical and temporal structure in the Neolithic period; the complex nature by which metallurgy was introduced to the island in the Chalcolithic and Early Bronze Age; and signals of continuity between the Early Bronze and Late Iron Age periods.




    aDNA reveals a different demographic impact of the Neolithic transition in South and North of Spain

    Gloria Gonzalez1,*, Tassi Francesca1, Kirstin Henneberger2, Cecilio Barroso3, Arturo Lombera4, Ramon Fabregas4, Aurora Grandal5, Michael Hofreiter2, Guido Barbujani1

    1 Biology, University of Ferrara, Ferrara., Italy,
    2 Biology, University of Potsdam, Potsdam, Germany,
    3 Archaeology, Fundacion Estudios Prehistoricos, Cordoba,
    4 Archaeology, Universtiy of Santiago de Compostela, Santiago de Compostela,
    5 Biology, University of A Coruna, A Coruna, Spain

    Abstract: Ancient DNA (aDNA) studies are strongly contributing to shed light on a widely debated topic in archaeology, anthropology and population genetics: the dynamics of the spread of farming into Europe, or Neolithic transition. In the last few years, nuclear aDNA from prehistoric samples have led to identify the genetic legacy of the Neolithic and later human migrations into modern Europeans. Far from closing the debate, these palaeogenomes are revealing a complicated scenario, where the demographic impact of the Neolithic transition seems to have been different in different geographic areas. Describing in detail how the transition occurred in each area, and by which combination of demic and cultural changes, is now an important research priority. The Iberian Peninsula, at the western edge of major human migrations is a particular interesting area for understanding otherwise elusiveaspects of European prehistory. We have taken advantage of the high percentage of endogenous DNA preserved in the petrous bone to recover nuclear genomes from Spanish prehistoric samples by shotgun sequencing. The newly generated genome data has revealed a different demographic impact of the Neolithic transition in North and South of Spain, with northern populations having a smaller Middle East component in their gene pool than southern populations. Furthermore, the palaeogenetic data has revealed prehistoric contacts between the Iberian and African populations dated back to at least 3000 years before present.

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    Finally found one of those that interests me: A genetic compendium of an island: documenting continuity and change across Irish prehistory.
     


    Hidden Content


    Y-DNA: R1b-FGC36982 (L21> DF13> Z39589> CTS2501> Z43690> Y8426> BY160> FGC36974>FGC36982)

    Additional Data:
    Lactase Persistent:
    rs4988235 AA (13910 TT)
    rs182549 TT (22018 AA)

    Red Hair Carrier:
    Arg160Trp+ (rs1805008 T) aka R160W

    Dad's mtDNA: K1a1

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    thanks rozenfeld good work, ancient and new dna are always good news even if what i'd really like to see is a lost battle

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    I'm extremely excited for some of these. That Iron Age Finnish DNA seems like it might reveal a lot about the spread of Uralic languages.

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    Quote Originally Posted by rozenfeld View Post
    The Role of Migration in Cultural Changes during the Chalcolithic period in the Levant

    Eadaoin Harney1,*, Hila May2, Israel Hershkovitz2, Dina Shalem3, Nadin Rohland4, Swapan Mallick4, Iosif Lazaridis4, Nick Patterson4 5, David Reich4 5 6

    1 Organismic and Evolutionary Biology, Harvard University, Cambridge, United States,
    2 Anatomy and Anthropology, Tel Aviv University, Tel Aviv,
    3 The Institute for Galilean Archaeology, Kinneret, Israel,
    4 Genetics, Harvard Medical School, Boston,
    5 Broad Institute, Cambridge,
    6 Howard Hughes Medical Institute, Boston, United States

    Abstract: A major controversy is whether cultural change evident in the archaeological record is typically achieved through movements of people or cultural infiltration. The Chalcolithic period in the southern Levant (4th-5th millennium BCE) contains artifacts not detected in earlier archaeological sites of the region, yet have strong affinities to contemporary and earlier cultures from Anatolia and Iran. In order to test the hypothesis that the Chalcolithic culture of this region may have been formed through migration from the North, we analyzed new genome-wide ancient DNA data from 22 individuals from the Peqi'in cave site in Upper Galilee, Israel that are associated with the Late Chalcolithic culture of the southern Levant, thereby approximately doubling the number of samples with genome-wide ancient human DNA from the Levant. We report that that these individuals derive approximately 58% of their ancestry from populations related to those of the local Levant Neolithic, approximately 17% from populations related to the Iran Chalcolithic, and approximately 25% related to the Anatolian Neolithic, supporting the hypothesis that this population was formed in part by migration from the North. We show that population turnover continued after the Chalcolithic, as the population that the Peqi'in Cave group was a part of did not contribute to later Levantine populations from the Bronze Age, which had little or no Anatolian-related ancestry.
    It seems they did not test Timnian remains, this is unfortunate since they probably did contribute to Jordan_EBA. The Anatolian-related admixture could be related to the Amuq valley PPNB.
    Last edited by Agamemnon; 06-30-2017 at 10:21 PM.
    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    The Genetic History of Northern Europe
    Alissa Mittnik 1 2,*, Chuan-Chao Wang 2, Saskia Pfrengle 1, Mantas Daubaras 3, Gunita Zarina 4, Fredrik Hallgren 5, Raili Allmäe 6, Vyacheslav Moiseyev 7, Valery Khartanovich 7, Anja Furtwängler 1, Aida Andrades Valtueńa 2, Michal Feldman 2, Christos Economou 8, Markku Oinonen 9, Andrejs Vasks 4, Mari Tőrv 10, Oleg Balanovsky 11 12, David Reich 13 14 15, Rimantas Jankauskas 16, Wolfgang Haak 2 17, Stephan Schiffels 2, Johannes Krause 1 2

    1Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, 2Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany, 3Department of Archaeology, Lithuanian Institute of History, Vilnius, Lithuania, 4Institute of Latvian History, Riga, Latvia, 5The Cultural Heritage Foundation, Västerĺs, Sweden, 6Archaeological Research Collection, Tallinn University, Tallinn, Estonia, 7Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russian Federation, 8Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden, 9Finnish Museum of Natural History - LUOMOS, University of Helsinki, Helsinki, Finland, 10Independent researcher, Tartu, Estonia, 11Research Centre for Medical Genetics, 12Vavilov Institute for General Genetics, Moscow, Russian Federation, 13Department of Genetics, 14Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 15Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States, 16Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius, Lithuania, 17School of Biological Sciences, The University of Adelaide, Adelaide, Australia

    Abstract: Recent genetic studies of ancient human genomes have revealed a complex population history of modern Europeans
    involving at least three major prehistoric migrations that were influenced by climatic conditions, the spread of technological and cultural innovations and possibly diseases. To what extent these dynamics also affected the very North of the European continent surrounding today’s Baltic Sea is less well understood.
    Here we report novel genome-wide DNA data from 24 ancient North Europeans ranging from ~7,500 to 200 BCE spanning the transition from a mobile hunter-gatherer to a sedentary agricultural lifestyle, as well as the adoption of bronze metallurgy. We co- analyze our data with over 300 available ancient genomes and data from around 3,800 modern individuals to show that the settlement of Scandinavia occurred via a southern and a northern route, and that the first Scandinavian Neolithic farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. We reveal that the range of Western European Mesolithic hunter- gatherers extended to the east of the Baltic Sea, where this population persisted without gene-flow from Central European farmers until around 2,900 BCE when the arrival of steppe pastoralists introduced a major shift in economy and established wide-reaching networks of contact within Europe during the Late Neolithic and Bronze Age. These, together with continued gene-flow from the local hunter-gatherer population led to the genetic makeup of today’s Lithuanian populations, while additional admixture related to Siberian and East Asian populations is needed to explain modern Estonians’ genetic composition.

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